Software
Volume measures for linkage disequilibrium
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* Corresponding author: Chiara Sabatti csabatti@mednet.ucla.edu
1 Department of Statistics, University of Illinois at Urbana-Champaign, Champaign IL 61820, USA
2 Department of Statistics, UCLA, Los Angeles CA 90095-1554, USA
3 Department of Human Genetics, UCLA, Los Angeles CA 90095-7088, USA
BMC Genetics 2006, 7:54 doi:10.1186/1471-2156-7-54
Published: 17 November 2006Abstract
Background
Defining measures of linkage disequilibrium (LD) that have good small sample properties and are applicable to multiallelic markers poses some challenges. The potential of volume measures in this context has been noted before, but their use has been hampered by computational challenges.
Results
We design a sequential importance sampling algorithm to evaluate volume measures on I × J tables. The algorithm is implemented in a C routine as a complement to exhaustive enumeration. We make the C code available as open source. We achieve fast and accurate evaluation of volume measures in two dimensional tables.
Conclusion
Applying our code to simulated and real datasets reinforces the belief that volume measures are a very useful tool for LD evaluation: they are not inflated in small samples, their definition encompasses multiallelic markers, and they can be computed with appreciable speed.